Package com.actelion.research.chem.descriptor.flexophore.generator

Class SubFlexophoreGenerator

java.lang.Object

com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator

public class SubFlexophoreGenerator
extends java.lang.Object

SubFlexophoreGenerator

Copyright: Actelion Ltd., Inc. All Rights Reserved This software is the proprietary information of Actelion Pharmaceuticals, Ltd. Use is subject to license terms.

Author:

Modest von Korff Oct 12, 2012 MvK: Start implementation

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SubFlexophoreGenerator.ViolatedConditionsCount

Constructor Summary

Constructors

Constructor	Description
SubFlexophoreGenerator(int minBinDistThresh, int maxDistanceBinThresh, int minNumDifferentInteractionTypes)

Method Summary

Modifier and Type	Method	Description
static java.util.List<MolDistHist>	generateSubPharmacophores(MolDistHist mdh, int size)
static java.util.List<MolDistHistViz>	generateSubPharmacophores(MolDistHistViz mdhv, int size)	Generates a list of sub-fragments.
static java.util.List<MolDistHistViz>	generateSubPharmacophores(MolDistHistViz mdhv, int minNumPPPoints, int maxNumPPPoints)
static java.util.List<MolDistHistViz>	generateSubPharmacophores(java.util.List<MolDistHistViz> liMDHV, int minNumPPPoints, int maxNumPPPoints)
java.util.List<MolDistHist>	generateSubPharmacophoresCheckedRange(MolDistHist mdh, int size)
static MolDistHist	getSubFragment(MolDistHist mdh, int[] arrIndices)
static MolDistHistVizFrag	getSubFragment(MolDistHistViz mdh, int[] arrIndices)
MolDistHist	getSubFragmentCheckedRange(MolDistHist mdh, int[] arrIndices)
static java.util.List<MolDistHistVizFrag>	getSubFragments(MolDistHistViz mdh, java.util.List<int[]> liIndices)	Inevitable pharmacophore points are considered (01.11.2012)
SubFlexophoreGenerator.ViolatedConditionsCount	getViolatedConditionsCount()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SubFlexophoreGenerator

public SubFlexophoreGenerator(int minBinDistThresh,
                              int maxDistanceBinThresh,
                              int minNumDifferentInteractionTypes)

Parameters:

minBinDistThresh -

maxDistanceBinThresh -

minNumDifferentInteractionTypes -

Method Detail

generateSubPharmacophoresCheckedRange

public java.util.List<MolDistHist> generateSubPharmacophoresCheckedRange(MolDistHist mdh,
                                                                         int size)

getSubFragmentCheckedRange

public MolDistHist getSubFragmentCheckedRange(MolDistHist mdh,
                                              int[] arrIndices)

getViolatedConditionsCount

public SubFlexophoreGenerator.ViolatedConditionsCount getViolatedConditionsCount()

generateSubPharmacophores

public static java.util.List<MolDistHistViz> generateSubPharmacophores(MolDistHistViz mdhv,
                                                                       int minNumPPPoints,
                                                                       int maxNumPPPoints)

generateSubPharmacophores

public static java.util.List<MolDistHistViz> generateSubPharmacophores(java.util.List<MolDistHistViz> liMDHV,
                                                                       int minNumPPPoints,
                                                                       int maxNumPPPoints)

generateSubPharmacophores

public static java.util.List<MolDistHistViz> generateSubPharmacophores(MolDistHistViz mdhv,
                                                                       int size)

Generates a list of sub-fragments.

Parameters:

mdhv -

size - number of pharmacophore points

Returns:

unique list of features

getSubFragments

public static java.util.List<MolDistHistVizFrag> getSubFragments(MolDistHistViz mdh,
                                                                 java.util.List<int[]> liIndices)

Inevitable pharmacophore points are considered (01.11.2012)

Parameters:

mdh -

liIndices - indices for pharmacophore points in mdh.

Returns:

getSubFragment

public static MolDistHistVizFrag getSubFragment(MolDistHistViz mdh,
                                                int[] arrIndices)

Parameters:

mdh -

arrIndices - the original index is set in the index field of the new SubFragment.

Returns:

generateSubPharmacophores

public static java.util.List<MolDistHist> generateSubPharmacophores(MolDistHist mdh,
                                                                    int size)

getSubFragment

public static MolDistHist getSubFragment(MolDistHist mdh,
                                         int[] arrIndices)